<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
          "DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
  <title>BIP.SDE.example</title>
  <link rel="stylesheet" href="epydoc.css" type="text/css" />
  <script type="text/javascript" src="epydoc.js"></script>
</head>

<body bgcolor="white" text="black" link="blue" vlink="#204080"
      alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
       bgcolor="#a0c0ff" cellspacing="0">
  <tr valign="middle">
  <!-- Home link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="BIP-module.html">Home</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Tree link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Index link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Help link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Project homepage -->
      <th class="navbar" align="right" width="100%">
        <table border="0" cellpadding="0" cellspacing="0">
          <tr><th class="navbar" align="center"
            ><a class="navbar" target="_top" href="http://code.google.com/p/bayesian-inference">Project Homepage</a></th>
          </tr></table></th>
  </tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
  <tr valign="top">
    <td width="100%">
      <span class="breadcrumbs">
        <a href="BIP-module.html">Package&nbsp;BIP</a> ::
        <a href="BIP.SDE-module.html">Package&nbsp;SDE</a> ::
        Module&nbsp;example
      </span>
    </td>
    <td>
      <table cellpadding="0" cellspacing="0">
        <!-- hide/show private -->
        <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
    onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
        <tr><td align="right"><span class="options"
            >[<a href="frames.html" target="_top">frames</a
            >]&nbsp;|&nbsp;<a href="BIP.SDE.example-pysrc.html"
            target="_top">no&nbsp;frames</a>]</span></td></tr>
      </table>
    </td>
  </tr>
</table>
<h1 class="epydoc">Source Code for <a href="BIP.SDE.example-module.html">Module BIP.SDE.example</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt>  <tt class="py-line"><tt class="py-comment"># -*- coding:utf-8 -*-</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt>  <tt class="py-line"><tt class="py-comment">#-----------------------------------------------------------------------------</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt>  <tt class="py-line"><tt class="py-comment"># Name:        example.py</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt>  <tt class="py-line"><tt class="py-comment"># Project:  Bayesian-Inference</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt>  <tt class="py-line"><tt class="py-comment"># Purpose:     </tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt>  <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt>  <tt class="py-line"><tt class="py-comment"># Author:      Fl&#225;vio Code&#231;o Coelho&lt;fccoelho@gmail.com&gt;</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt>  <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt>  <tt class="py-line"><tt class="py-comment"># Created:     2008-11-26</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt>  <tt class="py-line"><tt class="py-comment"># Copyright:   (c) 2008 by the Author</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt>  <tt class="py-line"><tt class="py-comment"># Licence:     GPL</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt>  <tt class="py-line"><tt class="py-comment">#-----------------------------------------------------------------------------</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt>  <tt class="py-line"><tt class="py-name">__docformat__</tt> <tt class="py-op">=</tt> <tt class="py-docstring">"restructuredtext en"</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt>  <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt>  <tt class="py-line"><tt class="py-string">Example of an SEIR model with two Infectious classes: subclinical(Is) and clinical(Ic)</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt>  <tt class="py-line"><tt class="py-string">        Is</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt>  <tt class="py-line"><tt class="py-string">       /  \</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt>  <tt class="py-line"><tt class="py-string">S -&gt; E     R</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt>  <tt class="py-line"><tt class="py-string">       \  /</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt>  <tt class="py-line"><tt class="py-string">        Ic</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt>  <tt class="py-line"><tt class="py-string">        </tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt>  <tt class="py-line"><tt class="py-string">States:</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt>  <tt class="py-line"><tt class="py-string">S: Susceptible</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt>  <tt class="py-line"><tt class="py-string">E: Exposed</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt>  <tt class="py-line"><tt class="py-string">Is: Infectious subclinical</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt>  <tt class="py-line"><tt class="py-string">Ic: Infectious clinical</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt>  <tt class="py-line"><tt class="py-string">R: Recovered</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt>  <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt>  <tt class="py-line"><tt class="py-string">Transition rates:</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt>  <tt class="py-line"><tt class="py-string">b,ks,kc,rs,rc = (0.001, 0.1, 0.1, 0.01, .01)</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt>  <tt class="py-line"><tt class="py-string">Transitions:</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt>  <tt class="py-line"><tt class="py-string">S -&gt; E : b*S*(Is+Ic)</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt>  <tt class="py-line"><tt class="py-string">E -&gt; Is : ks*E</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt>  <tt class="py-line"><tt class="py-string">E -&gt; Ic : kc*E</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt>  <tt class="py-line"><tt class="py-string">Is -&gt; R : rs*Is</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt>  <tt class="py-line"><tt class="py-string">Ic -&gt; R : rc*Ic</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt>  <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt>  <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">cgillespie</tt> <tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Class BIP.SDE.gillespie.Model=BIP.SDE.gillespie.Model-class.html,Class BIP.SMC.condensation.Model=BIP.SMC.condensation.Model-class.html"><a title="BIP.SDE.gillespie.Model
BIP.SMC.condensation.Model" class="py-name" href="#" onclick="return doclink('link-0', 'Model', 'link-0');">Model</a></tt> <tt class="py-keyword">as</tt> <tt class="py-name">CModel</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name" targets="Module BIP.SDE.gillespie=BIP.SDE.gillespie-module.html"><a title="BIP.SDE.gillespie" class="py-name" href="#" onclick="return doclink('link-1', 'gillespie', 'link-1');">gillespie</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name"><a title="BIP.SDE.gillespie.Model
BIP.SMC.condensation.Model" class="py-name" href="#" onclick="return doclink('link-2', 'Model', 'link-0');">Model</a></tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">time</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt>  <tt class="py-line"> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">array</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt>  <tt class="py-line"><tt id="link-3" class="py-name" targets="Variable BIP.SDE.example.vnames=BIP.SDE.example-module.html#vnames"><a title="BIP.SDE.example.vnames" class="py-name" href="#" onclick="return doclink('link-3', 'vnames', 'link-3');">vnames</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">'S'</tt><tt class="py-op">,</tt><tt class="py-string">'E'</tt><tt class="py-op">,</tt><tt class="py-string">'Is'</tt><tt class="py-op">,</tt><tt class="py-string">'Ic'</tt><tt class="py-op">,</tt><tt class="py-string">'R'</tt><tt class="py-op">]</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt>  <tt class="py-line"><tt class="py-comment">#rates: b,ks,kc,rs,rc</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt>  <tt class="py-line"> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt>  <tt class="py-line"><tt id="link-4" class="py-name" targets="Variable BIP.SDE.example.r=BIP.SDE.example-module.html#r"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-4', 'r', 'link-4');">r</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-number">0.001</tt><tt class="py-op">,</tt> <tt class="py-number">0.1</tt><tt class="py-op">,</tt> <tt class="py-number">0.1</tt><tt class="py-op">,</tt> <tt class="py-number">0.01</tt><tt class="py-op">,</tt> <tt class="py-number">.01</tt><tt class="py-op">)</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt>  <tt class="py-line"><tt id="link-5" class="py-name" targets="Variable BIP.SDE.example.ini=BIP.SDE.example-module.html#ini"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-5', 'ini', 'link-5');">ini</a></tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-number">490</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">10</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt>  <tt class="py-line"><tt class="py-comment"># propensity functions</tt> </tt>
<a name="f1"></a><div id="f1-def"><a name="L50"></a><tt class="py-lineno">50</tt> <a class="py-toggle" href="#" id="f1-toggle" onclick="return toggle('f1');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.SDE.example-module.html#f1">f1</a><tt class="py-op">(</tt><tt class="py-param">r</tt><tt class="py-op">,</tt><tt class="py-param">ini</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-keyword">return</tt> <tt id="link-6" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-6', 'r', 'link-4');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt id="link-7" class="py-name"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-7', 'ini', 'link-5');">ini</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt id="link-8" class="py-name"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-8', 'ini', 'link-5');">ini</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt id="link-9" class="py-name"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-9', 'ini', 'link-5');">ini</a></tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="f2"></a><div id="f2-def"><a name="L51"></a><tt class="py-lineno">51</tt> <a class="py-toggle" href="#" id="f2-toggle" onclick="return toggle('f2');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.SDE.example-module.html#f2">f2</a><tt class="py-op">(</tt><tt class="py-param">r</tt><tt class="py-op">,</tt><tt class="py-param">ini</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-keyword">return</tt> <tt id="link-10" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-10', 'r', 'link-4');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt id="link-11" class="py-name"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-11', 'ini', 'link-5');">ini</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
</div><a name="f3"></a><div id="f3-def"><a name="L52"></a><tt class="py-lineno">52</tt> <a class="py-toggle" href="#" id="f3-toggle" onclick="return toggle('f3');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.SDE.example-module.html#f3">f3</a><tt class="py-op">(</tt><tt class="py-param">r</tt><tt class="py-op">,</tt><tt class="py-param">ini</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-keyword">return</tt> <tt id="link-12" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-12', 'r', 'link-4');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt id="link-13" class="py-name"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-13', 'ini', 'link-5');">ini</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
</div><a name="f4"></a><div id="f4-def"><a name="L53"></a><tt class="py-lineno">53</tt> <a class="py-toggle" href="#" id="f4-toggle" onclick="return toggle('f4');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.SDE.example-module.html#f4">f4</a><tt class="py-op">(</tt><tt class="py-param">r</tt><tt class="py-op">,</tt><tt class="py-param">ini</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-keyword">return</tt> <tt id="link-14" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-14', 'r', 'link-4');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt id="link-15" class="py-name"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-15', 'ini', 'link-5');">ini</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
</div><a name="f5"></a><div id="f5-def"><a name="L54"></a><tt class="py-lineno">54</tt> <a class="py-toggle" href="#" id="f5-toggle" onclick="return toggle('f5');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.SDE.example-module.html#f5">f5</a><tt class="py-op">(</tt><tt class="py-param">r</tt><tt class="py-op">,</tt><tt class="py-param">ini</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-keyword">return</tt> <tt id="link-16" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-16', 'r', 'link-4');">r</a></tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt id="link-17" class="py-name"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-17', 'ini', 'link-5');">ini</a></tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
</div><a name="L55"></a><tt class="py-lineno">55</tt>  <tt class="py-line"> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt>  <tt class="py-line"><tt id="link-18" class="py-name" targets="Variable BIP.SDE.example.propf=BIP.SDE.example-module.html#propf"><a title="BIP.SDE.example.propf" class="py-name" href="#" onclick="return doclink('link-18', 'propf', 'link-18');">propf</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-19" class="py-name" targets="Function BIP.SDE.example.f1()=BIP.SDE.example-module.html#f1"><a title="BIP.SDE.example.f1" class="py-name" href="#" onclick="return doclink('link-19', 'f1', 'link-19');">f1</a></tt><tt class="py-op">,</tt><tt id="link-20" class="py-name" targets="Function BIP.SDE.example.f2()=BIP.SDE.example-module.html#f2"><a title="BIP.SDE.example.f2" class="py-name" href="#" onclick="return doclink('link-20', 'f2', 'link-20');">f2</a></tt><tt class="py-op">,</tt><tt id="link-21" class="py-name" targets="Function BIP.SDE.example.f3()=BIP.SDE.example-module.html#f3"><a title="BIP.SDE.example.f3" class="py-name" href="#" onclick="return doclink('link-21', 'f3', 'link-21');">f3</a></tt><tt class="py-op">,</tt><tt id="link-22" class="py-name" targets="Function BIP.SDE.example.f4()=BIP.SDE.example-module.html#f4"><a title="BIP.SDE.example.f4" class="py-name" href="#" onclick="return doclink('link-22', 'f4', 'link-22');">f4</a></tt><tt class="py-op">,</tt><tt id="link-23" class="py-name" targets="Function BIP.SDE.example.f5()=BIP.SDE.example-module.html#f5"><a title="BIP.SDE.example.f5" class="py-name" href="#" onclick="return doclink('link-23', 'f5', 'link-23');">f5</a></tt><tt class="py-op">)</tt> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt>  <tt class="py-line"> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt>  <tt class="py-line"><tt id="link-24" class="py-name" targets="Variable BIP.SDE.example.tmat=BIP.SDE.example-module.html#tmat"><a title="BIP.SDE.example.tmat" class="py-name" href="#" onclick="return doclink('link-24', 'tmat', 'link-24');">tmat</a></tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-comment">#S</tt> </tt>
<a name="L59"></a><tt class="py-lineno">59</tt>  <tt class="py-line">              <tt class="py-op">[</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-comment">#E</tt> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt>  <tt class="py-line">              <tt class="py-op">[</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-comment">#Is</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt>  <tt class="py-line">              <tt class="py-op">[</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-comment">#Ic</tt> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt>  <tt class="py-line">              <tt class="py-op">[</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-comment">#R</tt> </tt>
<a name="L63"></a><tt class="py-lineno">63</tt>  <tt class="py-line"><tt id="link-25" class="py-name" targets="Variable BIP.SDE.example.M=BIP.SDE.example-module.html#M"><a title="BIP.SDE.example.M" class="py-name" href="#" onclick="return doclink('link-25', 'M', 'link-25');">M</a></tt><tt class="py-op">=</tt><tt id="link-26" class="py-name"><a title="BIP.SDE.gillespie.Model
BIP.SMC.condensation.Model" class="py-name" href="#" onclick="return doclink('link-26', 'Model', 'link-0');">Model</a></tt><tt class="py-op">(</tt><tt id="link-27" class="py-name"><a title="BIP.SDE.example.vnames" class="py-name" href="#" onclick="return doclink('link-27', 'vnames', 'link-3');">vnames</a></tt><tt class="py-op">=</tt><tt id="link-28" class="py-name"><a title="BIP.SDE.example.vnames" class="py-name" href="#" onclick="return doclink('link-28', 'vnames', 'link-3');">vnames</a></tt><tt class="py-op">,</tt><tt class="py-name">rates</tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-29', 'r', 'link-4');">r</a></tt><tt class="py-op">,</tt><tt class="py-name">inits</tt><tt class="py-op">=</tt><tt id="link-30" class="py-name"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-30', 'ini', 'link-5');">ini</a></tt><tt class="py-op">,</tt><tt id="link-31" class="py-name"><a title="BIP.SDE.example.tmat" class="py-name" href="#" onclick="return doclink('link-31', 'tmat', 'link-24');">tmat</a></tt><tt class="py-op">=</tt><tt id="link-32" class="py-name"><a title="BIP.SDE.example.tmat" class="py-name" href="#" onclick="return doclink('link-32', 'tmat', 'link-24');">tmat</a></tt><tt class="py-op">,</tt><tt class="py-name">propensity</tt><tt class="py-op">=</tt><tt id="link-33" class="py-name"><a title="BIP.SDE.example.propf" class="py-name" href="#" onclick="return doclink('link-33', 'propf', 'link-18');">propf</a></tt><tt class="py-op">)</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt>  <tt class="py-line"><tt id="link-34" class="py-name" targets="Variable BIP.SDE.example.CM=BIP.SDE.example-module.html#CM"><a title="BIP.SDE.example.CM" class="py-name" href="#" onclick="return doclink('link-34', 'CM', 'link-34');">CM</a></tt> <tt class="py-op">=</tt> <tt class="py-name">CModel</tt><tt class="py-op">(</tt><tt id="link-35" class="py-name"><a title="BIP.SDE.example.vnames" class="py-name" href="#" onclick="return doclink('link-35', 'vnames', 'link-3');">vnames</a></tt><tt class="py-op">=</tt><tt id="link-36" class="py-name"><a title="BIP.SDE.example.vnames" class="py-name" href="#" onclick="return doclink('link-36', 'vnames', 'link-3');">vnames</a></tt><tt class="py-op">,</tt><tt class="py-name">rates</tt> <tt class="py-op">=</tt> <tt id="link-37" class="py-name"><a title="BIP.SDE.example.r" class="py-name" href="#" onclick="return doclink('link-37', 'r', 'link-4');">r</a></tt><tt class="py-op">,</tt><tt class="py-name">inits</tt><tt class="py-op">=</tt><tt id="link-38" class="py-name"><a title="BIP.SDE.example.ini" class="py-name" href="#" onclick="return doclink('link-38', 'ini', 'link-5');">ini</a></tt><tt class="py-op">,</tt><tt id="link-39" class="py-name"><a title="BIP.SDE.example.tmat" class="py-name" href="#" onclick="return doclink('link-39', 'tmat', 'link-24');">tmat</a></tt><tt class="py-op">=</tt><tt id="link-40" class="py-name"><a title="BIP.SDE.example.tmat" class="py-name" href="#" onclick="return doclink('link-40', 'tmat', 'link-24');">tmat</a></tt><tt class="py-op">,</tt><tt class="py-name">propensity</tt><tt class="py-op">=</tt><tt id="link-41" class="py-name"><a title="BIP.SDE.example.propf" class="py-name" href="#" onclick="return doclink('link-41', 'propf', 'link-18');">propf</a></tt><tt class="py-op">)</tt> </tt>
<a name="L65"></a><tt class="py-lineno">65</tt>  <tt class="py-line"> </tt>
<a name="L66"></a><tt class="py-lineno">66</tt>  <tt class="py-line"><tt class="py-comment"># timing python gillespie</tt> </tt>
<a name="L67"></a><tt class="py-lineno">67</tt>  <tt class="py-line"><tt id="link-42" class="py-name" targets="Variable BIP.SDE.example.t0=BIP.SDE.example-module.html#t0"><a title="BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-42', 't0', 'link-42');">t0</a></tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno">68</tt>  <tt class="py-line"><tt id="link-43" class="py-name"><a title="BIP.SDE.example.M" class="py-name" href="#" onclick="return doclink('link-43', 'M', 'link-25');">M</a></tt><tt class="py-op">.</tt><tt id="link-44" class="py-name" targets="Method BIP.Bayes.Melding.FitModel.run()=BIP.Bayes.Melding.FitModel-class.html#run,Method BIP.Bayes.Melding.Meld.run()=BIP.Bayes.Melding.Meld-class.html#run,Method BIP.SDE.gillespie.Model.run()=BIP.SDE.gillespie.Model-class.html#run"><a title="BIP.Bayes.Melding.FitModel.run
BIP.Bayes.Melding.Meld.run
BIP.SDE.gillespie.Model.run" class="py-name" href="#" onclick="return doclink('link-44', 'run', 'link-44');">run</a></tt><tt class="py-op">(</tt><tt class="py-name">tmax</tt><tt class="py-op">=</tt><tt class="py-number">80</tt><tt class="py-op">,</tt><tt class="py-name">reps</tt><tt class="py-op">=</tt><tt class="py-number">100</tt><tt class="py-op">,</tt><tt class="py-name">viz</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">serial</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno">69</tt>  <tt class="py-line"><tt id="link-45" class="py-name" targets="Variable BIP.SDE.example.pt=BIP.SDE.example-module.html#pt"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-45', 'pt', 'link-45');">pt</a></tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt id="link-46" class="py-name"><a title="BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-46', 't0', 'link-42');">t0</a></tt> </tt>
<a name="L70"></a><tt class="py-lineno">70</tt>  <tt class="py-line"><tt class="py-keyword">print</tt> <tt class="py-string">'Python total time: '</tt><tt class="py-op">,</tt><tt id="link-47" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-47', 'pt', 'link-45');">pt</a></tt><tt class="py-op">,</tt> <tt class="py-string">' seconds.'</tt> </tt>
<a name="L71"></a><tt class="py-lineno">71</tt>  <tt class="py-line"><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-name">series</tt><tt class="py-op">,</tt><tt class="py-name">steps</tt> <tt class="py-op">=</tt> <tt id="link-48" class="py-name"><a title="BIP.SDE.example.M" class="py-name" href="#" onclick="return doclink('link-48', 'M', 'link-25');">M</a></tt><tt class="py-op">.</tt><tt id="link-49" class="py-name" targets="Method BIP.SDE.gillespie.Model.getStats()=BIP.SDE.gillespie.Model-class.html#getStats"><a title="BIP.SDE.gillespie.Model.getStats" class="py-name" href="#" onclick="return doclink('link-49', 'getStats', 'link-49');">getStats</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno">72</tt>  <tt class="py-line"><tt class="py-keyword">print</tt> <tt class="py-name">steps</tt><tt class="py-op">,</tt><tt class="py-string">'steps'</tt> </tt>
<a name="L73"></a><tt class="py-lineno">73</tt>  <tt class="py-line"><tt class="py-comment"># timing cython gillespie</tt> </tt>
<a name="L74"></a><tt class="py-lineno">74</tt>  <tt class="py-line"><tt id="link-50" class="py-name"><a title="BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-50', 't0', 'link-42');">t0</a></tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno">75</tt>  <tt class="py-line"><tt id="link-51" class="py-name"><a title="BIP.SDE.example.CM" class="py-name" href="#" onclick="return doclink('link-51', 'CM', 'link-34');">CM</a></tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="BIP.Bayes.Melding.FitModel.run
BIP.Bayes.Melding.Meld.run
BIP.SDE.gillespie.Model.run" class="py-name" href="#" onclick="return doclink('link-52', 'run', 'link-44');">run</a></tt><tt class="py-op">(</tt><tt class="py-name">tmax</tt><tt class="py-op">=</tt><tt class="py-number">80</tt><tt class="py-op">,</tt><tt class="py-name">reps</tt><tt class="py-op">=</tt><tt class="py-number">100</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno">76</tt>  <tt class="py-line"><tt id="link-53" class="py-name" targets="Variable BIP.SDE.example.ct=BIP.SDE.example-module.html#ct"><a title="BIP.SDE.example.ct" class="py-name" href="#" onclick="return doclink('link-53', 'ct', 'link-53');">ct</a></tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt id="link-54" class="py-name"><a title="BIP.SDE.example.t0" class="py-name" href="#" onclick="return doclink('link-54', 't0', 'link-42');">t0</a></tt> </tt>
<a name="L77"></a><tt class="py-lineno">77</tt>  <tt class="py-line"><tt class="py-keyword">print</tt> <tt class="py-string">'Cython total time: '</tt><tt class="py-op">,</tt><tt id="link-55" class="py-name"><a title="BIP.SDE.example.ct" class="py-name" href="#" onclick="return doclink('link-55', 'ct', 'link-53');">ct</a></tt><tt class="py-op">,</tt> <tt class="py-string">' seconds.'</tt> </tt>
<a name="L78"></a><tt class="py-lineno">78</tt>  <tt class="py-line"><tt class="py-name">t2</tt><tt class="py-op">,</tt><tt class="py-name">series2</tt><tt class="py-op">,</tt><tt class="py-name">steps2</tt> <tt class="py-op">=</tt> <tt id="link-56" class="py-name"><a title="BIP.SDE.example.CM" class="py-name" href="#" onclick="return doclink('link-56', 'CM', 'link-34');">CM</a></tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="BIP.SDE.gillespie.Model.getStats" class="py-name" href="#" onclick="return doclink('link-57', 'getStats', 'link-49');">getStats</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno">79</tt>  <tt class="py-line"><tt class="py-keyword">print</tt> <tt class="py-name">steps2</tt><tt class="py-op">,</tt><tt class="py-string">' steps'</tt> </tt>
<a name="L80"></a><tt class="py-lineno">80</tt>  <tt class="py-line"><tt class="py-keyword">print</tt> <tt class="py-string">"Cython speedup: %sx"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt id="link-58" class="py-name"><a title="BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-58', 'pt', 'link-45');">pt</a></tt><tt class="py-op">/</tt><tt id="link-59" class="py-name"><a title="BIP.SDE.example.ct" class="py-name" href="#" onclick="return doclink('link-59', 'ct', 'link-53');">ct</a></tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno">81</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">pylab</tt> <tt class="py-keyword">import</tt> <tt class="py-name">plot</tt> <tt class="py-op">,</tt> <tt class="py-name">show</tt><tt class="py-op">,</tt> <tt class="py-name">legend</tt><tt class="py-op">,</tt> <tt class="py-name">errorbar</tt><tt class="py-op">,</tt> <tt class="py-name">title</tt><tt class="py-op">,</tt> <tt class="py-name">figure</tt> </tt>
<a name="L82"></a><tt class="py-lineno">82</tt>  <tt class="py-line"><tt class="py-comment">#print series.var(axis=0)</tt> </tt>
<a name="L83"></a><tt class="py-lineno">83</tt>  <tt class="py-line"><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-name">series</tt><tt class="py-op">.</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-string">'-o'</tt><tt class="py-op">)</tt> </tt>
<a name="L84"></a><tt class="py-lineno">84</tt>  <tt class="py-line"><tt class="py-name">title</tt><tt class="py-op">(</tt><tt class="py-string">'python curve'</tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno">85</tt>  <tt class="py-line"><tt class="py-name">legend</tt><tt class="py-op">(</tt><tt id="link-60" class="py-name"><a title="BIP.SDE.example.vnames" class="py-name" href="#" onclick="return doclink('link-60', 'vnames', 'link-3');">vnames</a></tt><tt class="py-op">,</tt><tt class="py-name">loc</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L86"></a><tt class="py-lineno">86</tt>  <tt class="py-line"><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L87"></a><tt class="py-lineno">87</tt>  <tt class="py-line"><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">t2</tt><tt class="py-op">,</tt><tt class="py-name">series2</tt><tt class="py-op">.</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-string">'-o'</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno">88</tt>  <tt class="py-line"><tt class="py-name">title</tt><tt class="py-op">(</tt><tt class="py-string">'cython curve'</tt><tt class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno">89</tt>  <tt class="py-line"><tt class="py-name">legend</tt><tt class="py-op">(</tt><tt id="link-61" class="py-name"><a title="BIP.SDE.example.vnames" class="py-name" href="#" onclick="return doclink('link-61', 'vnames', 'link-3');">vnames</a></tt><tt class="py-op">,</tt><tt class="py-name">loc</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L90"></a><tt class="py-lineno">90</tt>  <tt class="py-line"><tt class="py-name">show</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L91"></a><tt class="py-lineno">91</tt>  <tt class="py-line"> </tt><script type="text/javascript">
<!--
expandto(location.href);
// -->
</script>
</pre>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
       bgcolor="#a0c0ff" cellspacing="0">
  <tr valign="middle">
  <!-- Home link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="BIP-module.html">Home</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Tree link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Index link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Help link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Project homepage -->
      <th class="navbar" align="right" width="100%">
        <table border="0" cellpadding="0" cellspacing="0">
          <tr><th class="navbar" align="center"
            ><a class="navbar" target="_top" href="http://code.google.com/p/bayesian-inference">Project Homepage</a></th>
          </tr></table></th>
  </tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
  <tr>
    <td align="left" class="footer">
    Generated by Epydoc 3.0.1 on Thu Jan  7 10:45:34 2010
    </td>
    <td align="right" class="footer">
      <a target="mainFrame" href="http://epydoc.sourceforge.net"
        >http://epydoc.sourceforge.net</a>
    </td>
  </tr>
</table>

<script type="text/javascript">
  <!--
  // Private objects are initially displayed (because if
  // javascript is turned off then we want them to be
  // visible); but by default, we want to hide them.  So hide
  // them unless we have a cookie that says to show them.
  checkCookie();
  // -->
</script>
</body>
</html>
